We propose and demonstrate a cross-talk free simultaneous measurement system for temperature and external refractive index (ERI) implemented by dual-cavity Fabry-Perot (FP) fiber interferometer. The sensing probe consists of two cascaded FP cavities formed with a short piece of multimode fiber (MMF) and a micro-air-gap made of hollow core fiber (HOF). The fabricated sensor head was ultra-compact; the total length of the sensing part was less than 600 μn. Since the reflection spectrum of the composite FP structures is given by the superposition of each cavity spectrum, the spectrum measured in the wavelength domain was analyzed in the Fourier or spatial frequency domain. The experimental results showed that temperature could be determined independently from the spatial frequency shift without being affected by the ERI, while the ERI could be also measured solely by monitoring the intensity variation in the spatial frequency spectrum. The ERI and the temperature sensitivities were approximately 16 dB/RIU for the 1.33-1.45 index range, and 8.9 nm/°C at low temperature and 14.6 nm/°C at high temperature, respectively. In addition, it is also demonstrated that the proposed dual-cavity FP sensor has potential for compensating any power fluctuation that might happen in the input light source. ©2009 Optical Society of America.